[gmx-users] help with g_hydorder and g_polystat

Emmanuel, Alaina A.E.Emmanuel at warwick.ac.uk
Thu May 2 10:57:34 CEST 2013

That's ok. Thank you for your help. In the meantime, I might see if g_h2order is a good substitute for g_hydorder.

Kind Regards,


From: gmx-users-bounces at gromacs.org [gmx-users-bounces at gromacs.org] on behalf of Justin Lemkul [jalemkul at vt.edu]
Sent: 01 May 2013 22:58
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] help with g_hydorder and g_polystat

On 5/1/13 8:44 AM, Emmanuel, Alaina wrote:
> No, using a trajectory file with g_hydorder hasn't made any difference. The error is still the same.
> When I use g_polystat, I use the following command:
> g_polystat_d -f file.xtc  -s file.tpr -n polymer_backbone.ndx  -p persist.xvg -o polystat.xvg
> Note: Using "polymer_backbone.ndx" yields fewer polymers with nan issues, than using the whole polymer structure in an index file.

The g_hydorder problem is a bug in the code and I have filed a bug report on
Redmine.  I have no insight into what's going on with g_polystat, sorry.



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080

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